What follows here is a more detailed explanation I posted to a bulletin board once about this program.
- - - [Science Aims] - - -
The experiment is called the Neutrino Factory, scheduled for construction some time from 2015. Its primary aim is to fire beams of neutrinos (fundamental particles) through the Earth's interior to detector stations on different continents. They're doing this to measure whether they change type en route (there are 3 types of neutrino) and data from this in turn will allow them to determine the neutrino's mass more accurately.
The reason they want to do this is that the neutrino is just about the most common particle in the universe (billions pass through your body every second) and its mass will influence such things as the evolution of the universe and the exact way matter was first formed in the 'big bang'. In fact, neutrinos make up one quarter of the types of matter particles specified in the current 'standard model' of physics. In order to progress to more advanced theories of physics, it is often crucial to know the properties of particles to high precision in order to distinguish between the slightly different predictions of alternative theories.
Actually the entire Neutrino Factory complex (estimated to cost at least $1.9bn) will have several scientific aims. The neutrinos are used for fundamental physics experiments, but the proton beam that is produced at the start (this hits the target rod at the beginning of the simulation you download) is also going to be used in experiments such as neutralising radioactive waste by transmuting the radioactive elements into stable ones, and providing a high intensity source of neutrons for 3D atomic microscopy. The muon beam that will be coming from the end of the section we are optimising can also be used as the basis for a 'muon collider', a machine that could produce the highest-energy collisions between fundamental particles ever made artificially.
You are simulating the part of the process where the proton beam hits the target rod and causes pions to be emitted, which decay into muons. These would then proceed to a storage ring and decay into electrons and the neutrinos that are used for experiments. This is a fairly critical part of the apparatus, which catches the pions and confines some of them into a beam while they decay. The efficiency of this dictates that of the entire machine because it is built of a lot of acceleration stages 'in series' with each other. Whether the project eventually gets funded to be built depends on what levels of performance can be achieved with the designs generated during the present R&D. However, users of this program have already doubled the estimated efficiency of one stage and more are to be optimised in the future.